PXD022688

PXD022688 is an original dataset announced via ProteomeXchange.

Title	SP3 protocol for proteomic plant sample preparation prior LC-MS/MS
Description	Quantitative protein extraction from biological samples, as well as contaminants removal before LC-MS/MS, is fundamental for the successful bottom-up proteomic analysis. Four sample preparation methods, including the filter-aided sample preparation (FASP), two single-pot solid-phase-enhanced sample preparations (SP3) on carboxylated or HILIC paramagnetic beads, and protein suspension trapping method (S-Trap) were evaluated for SDS removal from Arabidopsis thaliana (AT) lysate. Finally, the optimized carboxylated SP3 workflow was benchmarked closely against the routine FASP. Ultimately, LC-MS/MS analyses revealed that regarding the number of identifications, number of missed cleavages, proteome coverage, repeatability, reduction of handling time, and cost per assay, the SP3 on carboxylated magnetic particles proved to be the best alternative for SDS and other contaminants removal from plant sample lysate. A robust and efficient two-hour SP3 protocol for a wide range of protein input is presented, benefiting from no need to adjust amount of beads, binding and rinsing conditions, or digestion parameters.
HostingRepository	PRIDE
AnnounceDate	2021-02-26
AnnouncementXML	Submission_2021-06-28_06:19:48.747.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Kamil Mikulasek
SpeciesList	scientific name: Arabidopsis thaliana (Mouse-ear cress); NCBI TaxID: 3702;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue; deamidated residue
Instrument	Q Exactive HF; LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2020-11-24 07:50:05	ID requested
1	2021-02-25 22:50:06	announced
⏵ 2	2021-06-28 06:19:49	announced	2021-06-28: Updated publication reference for PubMed record(s): 33777071.

Mikul, á, š, ek K, Kone, č, n, á H, Pot, ě, š, il D, Hol, á, nkov, á R, Havli, š J, Zdr, á, hal Z, SP3 Protocol for Proteomic Plant Sample Preparation Prior LC-MS/MS. Front Plant Sci, 12():635550(2021) [pubmed]

submitter keyword: bottom-up, protein cleanup, Arabidopsis thaliana, SDS removal, SP3, carboxylated magnetic beads, FASP, mass spectrometry

Zbyněk Zdráhal
contact affiliation	Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
contact email	zdrahal@sci.muni.cz
lab head
Kamil Mikulasek
contact affiliation	Proteomics Core Facility and Research Group Proteomics CEITEC-MU Masaryk University Brno, Czech Republic
contact email	357352@mail.muni.cz
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/02/PXD022688

PRIDE project URI

• PRIDE
  1. PXD022688
     1. Label: PRIDE project
     2. Name: SP3 protocol for proteomic plant sample preparation prior LC-MS/MS